At the close of last season, Captain Picard had been captured by the Borg. As the new season begins, his captors have mutilated him into a half-Borg, half-human called Locutus, and have been manipulating him to gain insight into human behavior to aid their plan to conquer Earth and enslave humanity. They have also accessed Picard's extensive knowledge of the U.S.S. Enterprise, its crew, and their strategy to defend Earth.

In Picard's absence, Fleet Admiral Hanson promotes First Officer Riker to captain. Riker finds the adjustment painful and difficult, but eventually takes the captain's chair and names Lieutenant Commander Shelby as his First Officer despite their initially hostile relationship. The new captain then commands his ship toward a rendezvous with Starfleet. En route, the crew is horrified by the discovery of a literal graveyard of Starfleet ships, left behind as a grim sign of the Borg's path of destruction toward Earth.

Learning of their intentions to assimilate the culture and technology of the Enterprise through Picard/Locutus, Riker realizes he can use his former captain to foil the Borg. He searches for a way to use Picard/Locutus to access Borg information in the same way the Borg tapped the captain for U.S.S. Enterprise secrets.

As the Borg ship races toward Earth, Data attempts to use Picard/Locutus as a communications link to the enemy. With time running out, Riker must make an agonizing choice between Data's desperate attempt to end the Borg advance, or sending the U.S.S. Enterprise on a collision course with the enemy ship to stop them from reaching Earth.